Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_011841100.1 RSPH17029_RS07895 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000015985.1:WP_011841100.1 Length = 397 Score = 230 bits (587), Expect = 5e-65 Identities = 133/343 (38%), Positives = 195/343 (56%), Gaps = 5/343 (1%) Query: 54 ARFSGDQQGMTYSRLQNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHL 113 A+++G +G TY+R +P E+L ++I LEGAE SGMAA+ A LL L AGDH+ Sbjct: 45 AQYAGQVKGFTYAREGHPNAEVLARKIDALEGAEGGIVVGSGMAAVAAVLLGLLRAGDHV 104 Query: 114 IGGRAAFGSCRWLTDTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVV 173 +GG +G + LP+ GI T++ DA D A+RP TK+ E +NPT+ V Sbjct: 105 VGGDQLYGRSLRMMAEDLPRLGIATSLADATDAAAVEAALRPETKLVLIEVVSNPTLRVA 164 Query: 174 DLKAVCAIARERGIVTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAV-CG 232 DL + A+ R RGI+ VD+ F+TP RP D GAD+V +S TK++ G V G V C Sbjct: 165 DLDGIAALCRARGILLAVDSTFSTPRGIRPFDHGADIVIHSVTKLLAGHSDVTLGYVACR 224 Query: 233 TEEFINNTLLPFHRNTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVP 290 T E + + F TG T SPF+ W+ +GL + LR R E A ++A L G V Sbjct: 225 TAE-LRRAVELFAVTTGLTPSPFDCWLAERGLLSFHLRYDRAEETAARLADHLAGLPGVR 283 Query: 291 RVNFPGLPSHPQHNLAMSQMA-AAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRS 349 RV +P HP A++ + G + S EL+GGR A+ L A+ + + +GD + Sbjct: 284 RVIYPLRADHPDQARAVALLGRRGGNMLSFELEGGRAAANALTRAMPAVAFAPTLGDVGT 343 Query: 350 LMTHPASTTHSGVAEDQRLLMGVGEGMLRLNVGLEDPEDLIAD 392 ++HPAS++H VA + R +G+ EG R++VG+E+ + LI D Sbjct: 344 TLSHPASSSHRAVAPEVRARLGISEGFFRISVGVEEADLLIRD 386 Lambda K H 0.319 0.134 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 352 Number of extensions: 12 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 402 Length of database: 397 Length adjustment: 31 Effective length of query: 371 Effective length of database: 366 Effective search space: 135786 Effective search space used: 135786 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 16 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory